Stays in the editor

What a script can't reach: zoom, panels, playback, saving.

The engine owns the document and the editing context. What's left is the editor's own: how you look at your work, and the app around it.

View: zoom, pan, grids, tiled view, onion skin. How the canvas is shown, not what's on it.
Panels and layout. Window chrome; there's nothing for a headless engine to show.
Playback. Previewing the animation. Frame durations and tags are scriptable.
Clipboard. App-level and not undoable. Scripts copy with app.getImage / app.putImage and app.moveCels / app.linkCels.
Open sprites, projects, sprite names, saving and export. App-level and irreversible, so a shared script can't close, delete or overwrite your work. A script edits the open sprite, as one undo step.
Importing reference images. A file picker. Reference layers can still be read and repositioned.
The saved brush and palette libraries. What you saved to your account; the engine can't see them, so a script gets one only when its config form asks and you pick it (brush and palette fields). Scripts also define their own brushes in the engine (app.defineBrush) — those aren't saved or added to the library.
The active tool. In the engine the tools are commands (app.drawStroke, app.floodFill, …).